Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	866,495	G→A	12.4%	C346Y (TGT→TAT)	rnr →	Ribonuclease R

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	866,495	0	G	A	12.4%	138.0 / 8.0	48	C346Y (TGT→TAT)	rnr	Ribonuclease R
Reads supporting (aligned to +/- strand):  ref base G (25/17);  new base A (3/3);  total (28/20)
Fisher's exact test for biased strand distribution p-value = 6.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

GATAGAGCGACAAGTGTATATCTTGTTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAGGATCCTAACATTCGCG  >  USA300TCH1516_ALE/866383‑866626                                                                                                                 |                                                                                                                                    gagagagCGACAAGTGTATATCTTGTTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTcgc                                                                                                         <  2:50585/138‑1 (MQ=255) gATAGAGCGACAAGTGTATATCTTGTTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTcgc                                                                                                         <  2:89966/141‑1 (MQ=255) gATAGAGCGACAAGTGTATATCTTGTTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTcgc                                                                                                         <  2:169810/141‑1 (MQ=255) gATAGAGCGACAAGTGTATATCTTGTTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTcgc                                                                                                         <  2:380658/141‑1 (MQ=255) gATAGAGCGACAAGTGTATATCTTGTTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTcgc                                                                                                         <  2:103315/141‑1 (MQ=255) gATAGAGCGACAAGTGTATATCTTGTTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTcgc                                                                                                         <  2:432606/141‑1 (MQ=255)     gagCGACAAGTGTATATCTTGTTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTATCGCATGGAAATCGATGCTAGTGGTCGCgttg                                                                                                     >  1:378453/1‑141 (MQ=255)     gagCGACAAGTGTATATCTTGTTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTATCGCATGGAAATCGATGCTAGTGGTCGCgttg                                                                                                     >  1:224835/1‑141 (MQ=255)     gagCGACAAGTGTATATCTTGTTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTATCGCATGGAAATCGATGCTAGTGGTCGCgttg                                                                                                     >  1:357906/1‑141 (MQ=255)          aCAAGTGTATATCTTGCTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCAGGGACAGCGATGCTAGTGGACGCGTTGCTaaa                                                                                                >  2:434912/1‑141 (MQ=255)             aGTGTATATCTTGTTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACAt                                                                                             <  1:15206/141‑1 (MQ=255)                    atCTTGTTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAGCATGAAAttt                                                                                      <  2:407279/141‑1 (MQ=255)                    atCTTGTTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAAttt                                                                                      <  1:320749/141‑1 (MQ=255)                          ttgACCATGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATa                                                                                >  2:218581/1‑141 (MQ=255)                               cGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGtt                                                                           <  2:443100/141‑1 (MQ=255)                               cGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGtt                                                                           <  2:115131/141‑1 (MQ=255)                                 tgtAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTtat                                                                         >  1:257530/1‑141 (MQ=255)                                 tgtAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTtat                                                                         >  1:257525/1‑141 (MQ=255)                                                 ccACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGa                                                         >  1:258583/1‑141 (MQ=255)                                                 ccACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGa                                                         >  1:101190/1‑141 (MQ=255)                                                 ccACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGa                                                         >  1:204975/1‑141 (MQ=255)                                                        gATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGt                                                  >  1:328992/1‑141 (MQ=255)                                                        gATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGt                                                  >  1:378268/1‑141 (MQ=255)                                                         aTTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTa                                                 <  2:257178/141‑1 (MQ=255)                                                           tAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTatg                                               >  1:455852/1‑141 (MQ=255)                                                           tAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTatg                                               >  2:342795/1‑141 (MQ=255)                                                              gTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTatgatg                                            >  1:277589/1‑141 (MQ=255)                                                                       tttGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATc                                   >  2:416773/1‑141 (MQ=255)                                                                       tttGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATc                                   >  2:288725/1‑141 (MQ=255)                                                                         tGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAg                                 >  2:151131/1‑141 (MQ=255)                                                                          gTTCATTGAATCCTAATGTTGATCGTTTAACTATAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGa                                <  2:239621/141‑1 (MQ=255)                                                                                    tCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGa                      <  2:257525/141‑1 (MQ=255)                                                                                    tCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGa                      <  2:257530/141‑1 (MQ=255)                                                                                     ccTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGaa                     >  1:257067/1‑141 (MQ=255)                                                                                        aaTGTTTATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAg                  >  1:371845/1‑141 (MQ=255)                                                                                        aaTGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAg                  >  2:60859/1‑141 (MQ=255)                                                                                        aaTGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAg                  >  2:153380/1‑141 (MQ=255)                                                                                        aaTGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAg                  >  2:60792/1‑141 (MQ=255)                                                                                             ttaTCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAGGATcc             <  1:189982/139‑1 (MQ=255)                                                                                             tGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAGGATcc             <  2:321105/141‑1 (MQ=255)                                                                                                 cGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAGGATCCTAAc         >  1:258479/1‑141 (MQ=255)                                                                                                     tAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAGGATCCTAACATTc     >  1:427878/1‑141 (MQ=255)                                                                                                       aCTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAGGATCCTAACATTcgc   >  1:416676/1‑141 (MQ=255)                                                                                                       aCTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAGGATCCTAACATTcgc   >  1:12025/1‑141 (MQ=255)                                                                                                       aCTCTAAGCTATCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAGGATCCTAACATTcgc   <  2:378453/141‑1 (MQ=255)                                                                                                       aCTCTAAGCTATCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAGGATCCTAACATTcgc   <  2:357906/141‑1 (MQ=255)                                                                                                       aCTCTAAGCTATCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAGGATCCTAACATTcgc   <  2:224835/141‑1 (MQ=255)                                                                                                        ctctAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTACATCAGATTATTACTCAACAGGATCATCACATTcgcg  >  2:116822/1‑141 (MQ=255)                                                                                                                 |                                                                                                                                    GATAGAGCGACAAGTGTATATCTTGTTGACCGTGTAATTCCAATGATTCCACATCGATTAAGTAATGGTATTTGTTCATTGAATCCTAATGTTGATCGTTTAACTCTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAAATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATTATTACTGAAAAGGATCCTAACATTCGCG  >  USA300TCH1516_ALE/866383‑866626

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑